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comparison callcodonvar.xml @ 9:18aad692772a draft default tip

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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="callcodonvar" name="Codon Variants" version="0.7.0"> 1 <tool id="callcodonvar" name="Codon Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description> 2 <description>Identifies codon variants and non-synonymous/synonymous mutations</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.0">quasitools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 cat $input_genes && 9 cat $input_genes &&
9 10
10 ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && 11 ln -s $input_bam '${input_bam.name}' &&
11 quasitools call codonvar $input_bam $ref_file $offset $input_genes 12 ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&
13
14 quasitools call codonvar '${input_bam.name}' $ref_file $offset $input_genes
12 15
13 #if $var_file: 16 #if $var_file:
14 $var_file 17 $var_file
15 #end if 18 #end if
16 19
54 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a 57 Call codon variants for a given BAM. A report is generated that details nucleotide variants within a
55 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to 58 codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to
56 a synonymous or non-synonymous mutation. 59 a synonymous or non-synonymous mutation.
57 60
58 ]]></help> 61 ]]></help>
59 <citations> 62 <expand macro="citations" />
60 <citation type="bibtex">
61 @misc{GitHubquasitoolscallcodonvar,
62 title = {quasitools callcodonvar},
63 publisher = {phac-nml},
64 journal = {GitHub repository},
65 url = {https://github.com/phac-nml/quasitools},
66 }
67 </citation>
68 </citations>
69 </tool> 63 </tool>